Exposing planktonic source communities from stream and floodplain ecosystems to differing hydraulic environments revealed strong selective hydraulic pressures but only minor founder effects on the differentiation of attached biofilms and suspended aggregates and their biodiversity dynamics. Key taxa with a coherent phylogenetic underpinning drove this differentiation. Few resident and phylogenetically related taxa formed the backbone of biofilm communities, whereas numerous taxa with lower temporal turnover characterized aggregate communities. Fundamental ecological differences between biofilms and aggregates exist and local hydraulics drives the distribution of microbial diversity along the fluvial continuum